note that these options will flatten comments and forms in a pdf file, making them uneditable
Schubert-It PDF Browser Plugin
(undocumented - top of my head) I think you need to print from the browser using this plugin, and it will circumvent any password protection from the printed file. Adobe Acrobat and Mac OS X will not print a protected PDF file to another PDF file.
this will not work if the security settings in the file prevent printing
this method does not respect form editing - the plugin allows you to modify protected forms in the browser, but you cannot create a pdf file with forms to edit in other programs
Postscript Conversion
When PDF documents are visible but not printable there's an easy workaround when you are using GNU/Linux. Print the pdf to postscript and back again.
pdftops in.pdf out.ps
pstopdf out.ps out.pdf
Ghostscript
(untested) You can use ghostscript directly with writePDF as the output format and just go pdf to pdf (pdftops is just a wrapper around ghostscript). If you have cygwin under windows, it has ghostscript and the other programs. It won't unlock fully encrypted PDFs (unless you DO have the password) but will emit something you can print or save.
I couldn't even find this output device, and gs doesn't seem to accept a pdf file as input. If it wants a ps file, then the Postscript Conversion method is probably best anyway.
ColorSync
(untested) On Mac OS X you can open your pdf in ColorSync and resave as pdf and it will remove any password protection. This does not work on pdfs that require password to open them. ColorSync is a free utility included with all versions of OS X.